A means of direct communication is established with Voyager allowing each crew member to speak with family and friends. The Doctor sends a holo-novel for publication based on a lost starship with a doctor who is treated like a slave, which causes controversy among the members of the ship.
Chakotay must convince Janeway and the other crew members of their past lives on Voyager. Matters are complicated when Chakotay is exposed and taken for interrogation.
When Voyager shuts down main power and interrupts the regeneration cycle of the Borg children, Neelix keeps them entertained by telling the story of why a certain section of Deck 12 is off-limits, and how the space-dwelling creature that lives there came aboard and "haunted" the ship.
News reaches Voyager through the up-and-running Pathfinder project that the Doctor's creator, Lewis Zimmerman, is critically ill. In an attempt to save his life, the Doctor's program is transmitted to the Alpha Quadrant, but once there, he finds Zimmerman does not want to be examined by an "obsolete" EMH program.
Seven becomes emotional when Icheb's parents are located, and it is assumed that he will leave Voyager to rejoin them. However, she later becomes increasingly concerned when it appears that they were not honest about the circumstances of his original assimilation.
A mysterious female alien contacts Voyager, claiming to be Ensign Lyndsay Ballard, who had been killed on an away mission years earlier.
The inhabitants of the holo-city of Fair Haven suspect the Voyager crew of having mystical powers when they witness the use of their futuristic technology.
Under attack by the territorial Turei, Voyager sets down on an uninhabited planet to hide and make repairs. In a cavern under the surface, they discover and revive the final remaining survivors of the Vaadwaur, the planet's original civilization, who had been in stasis for nearly 900 years. As Voyager and their new allies prepare to engage the Turei, there is reason to fear that the Vaadwaur are more dangerous than originally suspected.
The Doctor programs himself with the ability to daydream. When an alien spy gains access to The Doctor's visions he mistakes them for reality.
Voyager comes to the aid of the Equinox - another Federation starship also abducted by the Caretaker - now under attack by mysterious aliens from another dimension. As the two crews begin to work together to protect both ships, a dark secret lies hidden aboard the Equinox.
Sisko takes command of a new ship named in honor of the Defiant, while Kira, Garak and Damar barely survive a Dominion ambush on Cardassia Prime. Bashir and Ezri reveal their attractions for one another over coffee. Quark is appointed Zek's successor, and he is determined to overthrow new democratic changes that have just been implemented into Ferengi society. Garak, Damar and Kira successfully plant a bomb in Dominion barracks on Cardassia. In a shock turn of events, Zek appoints Rom as the new Grand Nagus of Ferenginar, despite Quark's earlier announcement.moreless
Captain Janeway relates the story of her distant ancestor, Shannon O'Donnell (Kate Mulgrew in a dual role), and her involvement in the construction of Earth's "Millennium Gate". She meets and falls in love with Henry Janeway - the one man standing in the way of the Gate's construction.
Voyager becomes trapped in an area of "chaotic space", where the laws of physics are in constant flux. Meanwhile, Chakotay suffers from hallucinations related to his holodeck boxing program. Although he is afraid he is losing his mind, Chakotay's hallucinations may be Voyager's only hope of learning how to escape from chaotic space.
After Paris and Torres tie the knot, the ship and its crew start to disintegrate on the molecular level.
Stardate: 51825.4 Nog and Jake are rescued by the U.S.S. Valiant when their ship is attacked by the Dominion while on their way to Ferenginar. The crew of the Valiant consists of the Starfleet Cadet corps known as 'Red Squad,' an elite band of cadets, after the main crew were killed when the Dominion War broke out. They decide to complete their mission, which Jake sees as suicide.moreless
Ensign Kim asks Tuvok to teach him Vulcan emotional control techniques when he falls in love with a holodeck character named Marayna. However, Kim soon becomes jealous when Marayna shows interest in Tuvok.
With the crew stranded on a barren planet, and the ship controlled by the Kazon, it's up to Tom Paris, Lon Suder, and The Doctor to retake Voyager and rescue their crewmates.
Seska lures Chakotay and Voyager to her, claiming that Maj Culluh is going to kill the baby she created using Chakotay's DNA, once he learns that it isn't his. Chakotay feels compelled to rescue his child, in spite of fearing it could be a trap.
Stardate: 49702.2 A pregnant Lwaxana Troi arrives on Deep Space Nine, distressed over the prospect of having her child taken away by its Tavnian father. In order to assist her in keeping her child in accordance with Tavnian law, Odo offers to marry her. Meanwhile, Jake finds inspiration in Onaya, an alien woman with sinister motives.moreless
When the Doctor is activated during a Red Alert, he learns that the ship has been abandoned, and that only B'Elanna Torres and an injured Captain Janeway are left on board. Soon afterwards, evidence starts to suggest that he is not, in fact, the EMH on Voyager, but actually its creator, Dr. Zimmerman, stuck in a malfunctioning holodeck on Jupiter Station.
After Sisko is promoted to Captain, he and the Defiant crew are manipulated by a Changeling posing as an ambassador.